ArticleProceedings. Biological sciences2023
Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.
Article in Proceedings. Biological sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 28 citations in OpenAlex.
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- Inferring temporal trends of multiple pathogens, variants, subtypes or serotypes from routine surveillance data.American journal of epidemiology · 2025Article
- SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.The Lancet. Microbe · 2025Observational
- Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution.Journal of virology · 2025Article
- Restoring flowcell type and basecaller configuration from FASTQ files of nanopore sequencing data.Nature communications · 2025Article
- Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes.medRxiv : the preprint server for health sciences · 2025Article
- Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.Virus evolution · 2025Article
- Article
- High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.Nature communications · 2024Article
- A speed limit on serial strain replacement from original antigenic sin.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Inferring community transmission of SARS-CoV-2 in the United Kingdom using the ONS COVID-19 Infection Survey.Infectious Disease Modelling · 2024Article
- Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana.Virus evolution · 2024Article
- Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.Proceedings. Biological sciences · 2023Article
- Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models.Molecular biology and evolution · 2023Article
- Development of primer-probe sets to rapidly distinguish single nucleotide polymorphisms in SARS-CoV-2 lineages.Frontiers in cellular and infection microbiology · 2023Article
- Elucidation of novel compounds and epitope-based peptide vaccine design against C30 endopeptidase regions of SARS-CoV-2 using immunoinformatics approaches.Frontiers in cellular and infection microbiology · 2023Article
- As the virus evolves, so too must we: a drug developer's perspective : We need a new paradigm in searching for next-generation countermeasures.Virology journal · 2022Review
- New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia.PLoS genetics · 2022Article
Corrections and comments
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Authors and funding
33 authors at 7 institutions in 2 countries.
Funding
Abstract
The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.